SOMO
SOMO reads the three ASAB1 output files and an additional file containing the look up data table-somo.par file which mostly contains information about each residue and how it is to be processed by the Trans routine. Example files can be found in the somo/examples directory.
ASAB1 output
The program is launched by calling SOMO with the provaly file name e.g. somo T-lyso. If you open the T-lyso file, the first three lines will look like: 1001 0.000000 T-lyso1 3.29400010.16400010.2660002.38800010.5330009.168000
The first number in the first line is 1001 which indicates the number of atoms in the model. The second value can be ignored for the moment. The final value is the name of the second of ASAB1 output file, in this case T-lyso1. Subsequent lines are the x, y and z coordinates for each atom. T-lyso1 contains information about the radius, mass and surface accessibilty code of each bead (1= surface atom, 6= buried side chain atom and 10 = buried main chain atom). 1.6500001511.870000131
The final file, T-lyso2 gives the atom name; the residue that it belongs to and residue name and number.. NLYSLYS_____1CALYSLYS_____1
Selecting algorithm
The first option is selecting the algorithm:
|
|
0 - for Trans |
|
|
1 - for AtoB |
In version 1 (v1) of SOMO, the trans algorithm (0) generates the model in three separate stages (1T,2T and 3T), whereas the AtoB algorithm (1) generates the model in two stages (1A and 2A).
Stages by which bead overlaps are removed
|
Stage |
Trans (T) |
AtoB (A) |
|
1 |
surface side chain beads with surface side chain beads |
surface beads with surface beads |
|
2 |
surface side chain beads with surface peptide beads and surface peptide beads with surface peptide beads |
surface beads with buried beads and buried beads with buriedbeads |
|
3 |
surface beads with buried beads and buried beads with buried beads |
|
Processing choices for Trans
Each stage offers four options for processing the model. They are:
|
|
0 - only remove overlaps |
|
|
1 - don't remove overlaps, but pop beads |
|
|
2 - remove overlaps and pop beads |
|
|
5 - do neither |
In Trans an extra option of translating surface side chain
beads away from the models centre of gravity is offered at the first
stage of processing. The extent of translation is equivalent to the
reduction in bead size as a result of overlap removal.
Processing choices for AtoB
Bead model generation with AtoB is processed in two stages: the first stage removing overlaps between beads representing residues encountered at the surface; the second being overlap removal between buried and surface beads. The choices used to generate the models are:
|
|
size of grid spacing |
|
|
using beads of variable or fixed radii |
SOMO output
Four output files are generated by SOMO: output (an option is available for changing the default name of output), ouput.rmc, output.rmc1 and INPUT.DAT. Except for the last file (which is printed on request and is formatted for use with HYDRO), the formats are compatible for running with RAZ, SUPC and some of the other program modules within BeaMS.
SOMO running, detailed description
When SOMO is
launched, it first ask you if you want to run it with the "default"
values specified in the "somo.cfg" file or if you want to
answer each prompt. You can edit the "somo.cfg" file with
any standard text editor to adapt it to your needs. Below we will
guide you through the various prompts.
The next prompt asks
if you want to use the parameters stored in the "somo.par"
file, that can be also edited to suit your needs. The "somo.par"
file contains all the values and rules used to generate and position
the beads, and it looks like this (with explanations at the end of
the table; the first number is the number of parameters-containing
lines, the second is the used volume for the water of hydration):
31
24.041
CB
XX XX XX XX 71.10 15 9 0 1.816
ALA 1
SG XX XX XX XX 103.20 47 2 0
2.183 CYS 1
OD1 OD2 XX XX XX 115.10 59 3 5 2.321
ASP 0
OE1 OE2 XX XX XX 129.10 73 3 6 2.643
GLU 0
CD2 CE1 XX XX XX 147.20 91 9 0 3.118
PHE 0
XX XX XX XX XX 57.10 0 0 0
0.000 GLY 2
ND1 NE2 XX XX XX 137.20 81 4 3
2.832 HIS 0
CB CG1 CG2 CD1 XX 113.20 57 9 0 2.870
ILE 0
CE NZ XX XX XX 128.20
73 4 3 2.902 LYS 0
CG XX XX XX XX 113.20
57 9 0 2.871 LEU 1
SD XX XX XX XX 131.20
75 9 1 2.899 MET 1
OD1 ND2 XX XX XX 114.10 58 2 1
2.426 ASN 0
CB CD XX XX XX 97.10
41 9 1 2.401 PRO 0
OE1 NE2 XX XX XX 128.10 72 2 1
2.722 GLN 0
NH1 NH2 XX XX XX 156.20 101 4 2
3.135 ARG 0
OG XX XX XX XX 87.10
31 2 1 1.938 SER 1
OG1 CG2 XX XX XX 101.10 45 2 1
2.382 THR 0
CB CG1 CG2 XX XX 99.10 43 9 0 2.606 VAL
0
CD1 CE3 CZ3 XX XX 186.20 130 9 1 3.391 TRP 0
CE1 CE2 XX XX XX 163.20 107 2 2 3.159
TYR 0
CB CD XX XX XX 71.10 15 9 0
1.816 PCA 1
C2 C6 XX XX XX 162.14 162
13 3 3.403 GAL 0
C2 C6 XX XX XX 162.14 162
13 3 3.403 MAN 0
C5 O5 C7 XX XX 203.19 203
13 3 3.771 NAG 0
C1 C8 C10 XX XX 291.96 292 13 9
4.062 SIA 0
C1 C4 XX XX XX 146.14 146
13 2 3.386 FUC 0
C2 C6 XX
XX XX 179.15 179
12 3 3.403 OG1 0
C7 C8 C9 C10 XX 56.11 56 14 0
2.880 OG2 0
C11 C12 C13 C14 XX 57.12 57 14 0
2.880 OG3 0
CA C O N XX 56
56 2 1 2.493 PEP 0
OXT XX XX XX XX 58 58 8 5 2.561
TER 0
#########################################################
Add comments only after this line:
number of residue lines to read, volume of water
atom names (5) columns - mol. wt. - mass of side chain - colour - hydration - radius - name - choice of baric methods.
The column size is fixed, however more rows can be added by writing in the extra row and modifying the value of the number on the 1st line. So at the mo. it has a value of 31 implying that there are 31 lines to read.
baric methods - 1 = baric1 (placing the bead at the position of the furthest atom specified in the p3 file)
0 = baric (placing the bead at the cog of atoms in the above list).
2 = neither function gets called.
Modifications
done to it: new values for the residue radii, calculated from
col
BL- of Table 7 of Tsai et al., JMB 290:253-266, 1999. Those are
derived
from
BURIED residues.
Chothia's water vol = 24.041
SOMO then reads the
ASAB1-generated files, and prompts the user for selecting between two
bead-generation routines, AtoB and TRANS. In the following, we will
explain how to run SOMO with the TRANS application, which generates
and positions beads according to the rules specified in the somo.par
file.
TRANS works in a hierarchical way, first treating accessible (“surface”) side chains, then accessible peptide bond segments, and finally all the non-accessible (“buried”) residues. Once the beads have been generated, overlaps between them must be removed, otherwise in the hydrodynamic computations the Oseen-Yamakawa-Bloomfield hydrodynamic interaction tensor, which was developed for non-overlapping beads of different radius (García de la Torre and Bloomfield, Q. Rev Biophys 14, 81-139, 1981), cannot be applied. The overlap removal is done in three steps, first between surface side chains beads, then between surface side chains and surface main chain beads, and finally between all the remaining beads including the buried ones. A hierarchical procedure is implemented in each step: each bead is checked against all the others, and the couples with overlaps are ranked in decreasing order. In the first two steps, it is possible to first fuse together (“popping”) beads overlapping by more than a user-selected threshold, and then proceed with the standard overlap removal, which is done by decreasing the radius of each bead in a couple by an amount proportional to its radius. In the first step, the user can also choose the “outward translation” routine, which was conceived to preserve as much as possible the original surface in the bead model while decreasing the radii of overlapping beads. Basically, the radius of each bead in the couple is reduced by a small increment (proportional the each one’s radius), and their centers are then translated outwardly by the same amount along the lines connecting them to the center of mass of the molecule. The procedure is repeated until the overlap is removed.
Accordingly, the
first prompt of the TRANS routine deals with surface side chains
beads, with four options currently available:
0 - remove overlaps asynchronously (--> i.e. hierarchically)
1 - pop beads but do not remove overlaps (--> fuse beads that overlap by more than a threshold but leave the overlaps; used for instance to generate a bead model with the beads positioned correctly, and then reduce the resolution using a grid like in AtoB)
2 - pop beads and remove overlaps asynchrounously (--> as in option 0, following the fusion of beads that overlap by more than a selected threshold; RECOMMENDED OPTION)
5 - neither (--> as in option 1, but without the fusion of beads that overlap by more than a selected threshold)
If options 0 or 2
are chosen, it is asked if the "outward translation"
routine should be used (we suggest to use it).
If options 1 or 2
are chosen, it is asked for the percentage of the overlaps above
which two beads will be fused (we recommend 70%, but we have not
fully explored this option).
Next the overlaps
between surface side chains and surface peptide bond beads, and
between surface peptide bond beads, are treated, with the same
options as above:
0 - remove overlaps asynchronously (--> i.e. hierarchically)
1 - pop beads but do not remove overlaps (--> fuse beads that overlap by more than a threshold but leave the overlaps; used for instance to generate a bead model with the beads positioned correctly, and then reduce the resolution using a grid like in AtoB)
2 - pop beads and remove overlaps asynchrounously (--> as in option 0, following the fusion of beads that overlap by more than a selected threshold; RECOMMENDED OPTION)
5 - neither (--> as in option 1, but without the fusion of beads that overlap by more than a selected threshold)
If options 1 or 2
are chosen, it is asked for the percentage of the overlaps above
which two beads will be fused (as above, we recommend 70%, but we
have not fully explored this option).
Finally, the
overlaps between buried beads are treated, again with the same range
of options:
0 - remove overlaps asynchronously (--> i.e. hierarchically; RECOMMENDED OPTION)
1 - pop beads but do not remove overlaps (--> fuse beads that overlap by more than a threshold but leave the overlaps; used for instance to generate a bead model with the beads positioned correctly, and then reduce the resolution using a grid like in AtoB)
2 - pop beads and remove overlaps asynchrounously (--> as in option 0, following the fusion of beads that overlap by more than a selected threshold)
5 - neither (--> as in option 1, but without the fusion of beads that overlap by more than a selected threshold)
If options 1 or 2
are chosen, it is asked for the percentage of the overlaps above
which two beads will be fused (we do NOT recommend options 1 or 2 at
this stage).
Next, there is a
prompt for using standard output filename ("output") or to
choose a different filename; if the latter is chosen, enter the
filename.
SOMO
will save the output coordinates and radii in either the HYDRO
(García de la Torre et al., Biophys J., 67, 530-531, 1994) or
BEAMS (Spotorno et al., Eur. Biophys. J. 25, 373-384 & 26, 417,
1997) formats for subsequent computation of the hydrodynamic
properties. In the BEAMS format, three files are produced, the first
two having the same format of the ASAB1-generated provaly (number of
beads, a “flag” number and a second filename, followed by the
coordinates) and provaly1 (radii, masses and colors, .rmc file)
files. The “flag” is used by the BEAMS programs to choose between
various options (among which variable or fixed radii, presence on the
first file of a value for the partial specific volume allowing the
computation of the sedimentation coefficient), and the colors are
used not only for visualization purposes, but also to selectively
remove some beads from the computations (beads color coded “0”
will always be excluded, while beads coded “6” can be included or
excluded). The third file is exactly like the second, but it has a
fourth column containing the correspondence between the original
residues and the beads, a very useful feature that allows to work
with the bead model as a lower-resolution structural model (.rmcoresp
file).
In the prompt asking for HYDRO or BEAMS format, there is also the option of saving the coordinates and associate information after a reordering of the output so that the residues are ordered in ascending order as in the original PDB file and preserving the chain separation for multiple chain structures. However, the beads will be still divided in blocks containing first those representing surface side chains, then surface peptide bonds, then buried side chains and finally buried peptide bonds. For memory reasons, this reordered output option should NOT be chosen for structures containing more than 3000 BEADS.
If either of the BEAMS formats is chosen, the last prompt asks for the possibility of printing in the file a value for the partial specific volume of the protein used then by SUPCW to compute the sedimentation coefficient. If this option is chosen, next enter the value of the psv.
The algorithm then starts, and its progress is constantly updated on the screen.
When the operations
are terminated, enter "1" if you want to visualize the
model using RAZ/Rasmol, or 0 to exit. The model should be then
rechecked using ASAB1 to control if during the overlap removal
routines some beads that were assigned to the buried category are
instead exposed. As the percentage of exposure above which the beads
are no longer considered buried, we suggest 30%, although this issue
has NOT been fully evaluated.
Last modified: September 2005